Change face instance orientation
As far as I understand the manual, when a face is created, its vertices are indexed on a per-face basis (not the same as the vertex indices for the whole mesh).
Contrarily to the mesh-wide vertex indices, These are not accessible or modifiable.
In other words, your only solution is to rotate each face by whatever multiple of 90° and then use the modeling tools to get back the original shape and ratio of the face.
Or, as suggested in the manual, restart your modeling and use face duplication instead of edge extrusion or some other operator in order to get more predictable results, and display the instances while modeling so you don't get surprised later.